Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Table 9 Genomic annotations and count of variants for Fayoumi vs. Leghorn: reference^a

Type (Fayoumi vs. Leghorn: reference^a)	Count
DOWNSTREAM	161,833
EXON	300
INTERGENIC	872,171
INTRON	812,038
NONE	2,121,836
NON_SYNONYMOUS_CODING	26,500
NON_SYNONYMOUS_START	16
SPLICE_SITE_ACCEPTOR	602
SPLICE_SITE_DONOR	634
START_GAINED	507
START_LOST	31
STOP_GAINED	1,511
STOP_LOST	53
SYNONYMOUS_CODING	21,093
SYNONYMOUS_START	21
SYNONYMOUS_STOP	27
UPSTREAM	158,646
UTR_3_PRIME	23,377
UTR_5_PRIME	3,428

ISSN: 1471-2164